low salt vs Control
jeff karnsomprot
2025-07-10
1 Loading in Data sets + Library packages.
##
## The downloaded binary packages are in
## /var/folders/7n/x74qctp91rng390gx0z9hmd80000gn/T//RtmpfyxiFj/downloaded_packages2 Loading Dataset
options(future.globals.maxSize = 74 * 1024^3) # 55 GB
getOption("future.globals.maxSize") #59055800320## [1] 79456894976SO4$sample <- factor(SO4$sample, levels = c("SO1", "SO4", "SO3", "SO2"))
VlnPlot(SO4,"S100g",split.by = "treatment",group.by = "sample")## The default behaviour of split.by has changed.
## Separate violin plots are now plotted side-by-side.
## To restore the old behaviour of a single split violin,
## set split.plot = TRUE.
##
## This message will be shown once per session.## Warning: The `slot` argument of `FetchData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning: `PackageCheck()` was deprecated in SeuratObject 5.0.0.
## ℹ Please use `rlang::check_installed()` instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# Macula Densa Markers , Nos1, Avpr1a, Slc12a1, Ptgs2, and Slc9a2
VlnPlot(SO4, c("Nos1","Avpr1a","Slc12a1","Ptgs2","Slc9a2","Pappa2"),split.by = "treatment",group.by = "treatment")
## Warning: The following arguments are not used: drop
3 Markers of control vs low_salt up/down regulation
Upregulated = low salt, positive, activated by low_salt Downregulated = control, negative, supressed of low_salt
Idents(SO4) <- "subclass2_MD"
subtypes <- c('type_1', 'type_2','type_3','type_4')
markers_list <- list()
# forloop markers for each subtype
for (subtype in subtypes) {
markers_list[[subtype]] <- FindMarkers(
object = SO4,
ident.1 = "low_salt",
ident.2 = "control",
group.by = "treatment",
subset.ident = subtype,
min.pct = 0.1,
logfc.threshold = 0.25,
only.pos = FALSE
)
}## Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
## (default method for FindMarkers) please install the presto package
## --------------------------------------------
## install.packages('devtools')
## devtools::install_github('immunogenomics/presto')
## --------------------------------------------
## After installation of presto, Seurat will automatically use the more
## efficient implementation (no further action necessary).
## This message will be shown once per session
##
## control low_salt
## type_1 3560 4950
## type_2 1302 994
## type_3 143 405
## type_4 42 834 Type 1
4.1 Type 1 Pathway Upregulated = Low salt
df<- type_1%>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers1up <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 4.01% of input gene IDs are fail to map...markers1up <- ENTREZ_list %>% inner_join(markers1up, by = "SYMBOL")
markers1up <- markers1up %>% dplyr::filter(p_val_adj < 0.05)
#head(markers, n = 50)
pos.markers1up <- markers1up %>% dplyr::filter(avg_log2FC > 0.5) %>% arrange(desc(abs(avg_log2FC)))
#change around avg log value
pos.ranks1up <- pos.markers1up$ENTREZID[abs(pos.markers1up$avg_log2FC) > 0]
#head(pos.ranks)
pos_go1up <- enrichGO(gene = pos.ranks1up, #a vector of entrez gene id
OrgDb = "org.Mm.eg.db",
ont = "BP",
readable = TRUE) #whether mapping gene ID to gene Name
pos_go1up## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:65] "16010" "239435" "23850" "19283" "211739" "70337" "19225" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...127 enriched terms found
## 'data.frame': 127 obs. of 12 variables:
## $ ID : chr "GO:0006469" "GO:0071560" "GO:0033673" "GO:0071559" ...
## $ Description : chr "negative regulation of protein kinase activity" "cellular response to transforming growth factor beta stimulus" "negative regulation of kinase activity" "response to transforming growth factor beta" ...
## $ GeneRatio : chr "7/61" "8/61" "7/61" "8/61" ...
## $ BgRatio : chr "178/28928" "281/28928" "191/28928" "288/28928" ...
## $ RichFactor : num 0.0393 0.0285 0.0366 0.0278 0.0326 ...
## $ FoldEnrichment: num 18.6 13.5 17.4 13.2 15.4 ...
## $ zScore : num 10.86 9.68 10.44 9.54 9.77 ...
## $ pvalue : num 9.78e-08 1.35e-07 1.58e-07 1.63e-07 3.53e-07 ...
## $ p.adjust : num 7.36e-05 7.36e-05 7.36e-05 7.36e-05 1.16e-04 ...
## $ qvalue : num 4.98e-05 4.98e-05 4.98e-05 4.98e-05 7.87e-05 ...
## $ geneID : chr "Cep85/Hspb1/Cdk5rap1/Cdkn1c/Bmp2/Rgs2/Spry1" "Fos/Cav2/Cdkn1c/Wnt10a/Bambi/Bmp2/Itgb8/Spry1" "Cep85/Hspb1/Cdk5rap1/Cdkn1c/Bmp2/Rgs2/Spry1" "Fos/Cav2/Cdkn1c/Wnt10a/Bambi/Bmp2/Itgb8/Spry1" ...
## $ Count : int 7 8 7 8 7 7 8 8 8 6 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722 chart1up <- dotplot(pos_go1up) +
ggtitle("type 1 upregulated lowsalt") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)) +
scale_y_discrete(position = "right",
labels = function(x) str_wrap(x, width = 25)) # Wrap y-axis labels to 2 lines## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
4.1.1 Type 1 Up Gene View
pathway_type1up <- strsplit(pos_go1up$geneID, "/")
names(pathway_type1up) <- pos_go1up$Description
pathway_type1up## $`negative regulation of protein kinase activity`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Cdkn1c" "Bmp2" "Rgs2" "Spry1"
##
## $`cellular response to transforming growth factor beta stimulus`
## [1] "Fos" "Cav2" "Cdkn1c" "Wnt10a" "Bambi" "Bmp2" "Itgb8" "Spry1"
##
## $`negative regulation of kinase activity`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Cdkn1c" "Bmp2" "Rgs2" "Spry1"
##
## $`response to transforming growth factor beta`
## [1] "Fos" "Cav2" "Cdkn1c" "Wnt10a" "Bambi" "Bmp2" "Itgb8" "Spry1"
##
## $`negative regulation of transferase activity`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Cdkn1c" "Bmp2" "Rgs2" "Spry1"
##
## $`transforming growth factor beta receptor signaling pathway`
## [1] "Fos" "Cav2" "Cdkn1c" "Bambi" "Bmp2" "Itgb8" "Spry1"
##
## $`transforming growth factor beta receptor superfamily signaling pathway`
## [1] "Fos" "Cav2" "Cdkn1c" "Bambi" "Hfe" "Bmp2" "Itgb8" "Spry1"
##
## $`negative regulation of phosphorus metabolic process`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Cdkn1c" "Bmp2" "Rgs2" "Aldob"
## [8] "Spry1"
##
## $`negative regulation of phosphate metabolic process`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Cdkn1c" "Bmp2" "Rgs2" "Aldob"
## [8] "Spry1"
##
## $`regulation of epithelial cell differentiation`
## [1] "Sfn" "Cdkn1c" "F11r" "Bmp2" "Etv4" "Spry1"
##
## $`cell surface receptor protein serine/threonine kinase signaling pathway`
## [1] "Fos" "Cav2" "Cdkn1c" "Bambi" "Hfe" "Bmp2" "Itgb8" "Spry1"
##
## $`negative regulation of protein phosphorylation`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Cdkn1c" "Bmp2" "Rgs2" "Spry1"
##
## $`negative regulation of phosphorylation`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Cdkn1c" "Bmp2" "Rgs2" "Spry1"
##
## $`regulation of protein kinase activity`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Sfn" "Cdkn1c" "Bmp2" "Rgs2"
## [8] "Spry1"
##
## $`skeletal muscle organ development`
## [1] "Mcub" "Fos" "Cav2" "Btg2" "Hspa8" "Mymx"
##
## $`regulation of transforming growth factor beta receptor signaling pathway`
## [1] "Cav2" "Cdkn1c" "Bambi" "Bmp2" "Spry1"
##
## $`regulation of cellular response to transforming growth factor beta stimulus`
## [1] "Cav2" "Cdkn1c" "Bambi" "Bmp2" "Spry1"
##
## $`protein refolding`
## [1] "Hspb1" "Hspa8" "Hspa1a"
##
## $`muscle organ development`
## [1] "Mcub" "Fos" "Cav2" "Btg2" "Hspa8" "Mymx" "Bmp2"
##
## $`regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cav2" "Cdkn1c" "Bambi" "Hfe" "Bmp2" "Spry1"
##
## $`negative regulation of protein modification process`
## [1] "Cep85" "Hspb1" "Cdk5rap1" "Cdkn1c" "Bmp2" "Rgs2" "Spry1"
##
## $`negative regulation of protein serine/threonine kinase activity`
## [1] "Cdk5rap1" "Bmp2" "Rgs2" "Spry1"
##
## $`response to heat`
## [1] "Ptgs2" "Hspb1" "Hspa8" "Hspa1a"
##
## $`negative regulation of transforming growth factor beta receptor signaling pathway`
## [1] "Cav2" "Bambi" "Bmp2" "Spry1"
##
## $`cellular response to metal ion`
## [1] "Ptgs2" "Fos" "Chp2" "Hspa8" "Hfe"
##
## $`skeletal muscle tissue development`
## [1] "Mcub" "Fos" "Cav2" "Btg2" "Hspa8"
##
## $`response to toxic substance`
## [1] "Ptgs2" "Lcn2" "Fos" "Ptges" "Pon2"
##
## $regeneration
## [1] "Mcub" "Mymx" "Scarf1" "Hfe" "Cspg5"
##
## $`cell-substrate adhesion`
## [1] "Ptprz1" "Frem1" "Bcl6" "Limch1" "Itgb8" "Cspg5"
##
## $`response to metal ion`
## [1] "Ptgs2" "Fos" "Chp2" "Hspa8" "Hfe" "Aldob"
##
## $`acute-phase response`
## [1] "Ptgs2" "Ptges" "Hfe"
##
## $`regulation of cyclin-dependent protein kinase activity`
## [1] "Cdk5rap1" "Sfn" "Cdkn1c"
##
## $`negative regulation of MAP kinase activity`
## [1] "Bmp2" "Rgs2" "Spry1"
##
## $`regulation of NADP metabolic process`
## [1] "Me1" "Aldob"
##
## $`regulation of lens fiber cell differentiation`
## [1] "Cdkn1c" "Spry1"
##
## $`response to phorbol 13-acetate 12-myristate`
## [1] "Fos" "Btg2"
##
## $`cellular response to phorbol 13-acetate 12-myristate`
## [1] "Fos" "Btg2"
##
## $`positive regulation of phosphatase activity`
## [1] "Chp2" "Bmp2"
##
## $`regulation of fever generation`
## [1] "Ptgs2" "Ptges"
##
## $`regulation of protein serine/threonine kinase activity`
## [1] "Cdk5rap1" "Sfn" "Bmp2" "Rgs2" "Spry1"
##
## $`negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cav2" "Bambi" "Bmp2" "Spry1"
##
## $`positive regulation of dephosphorylation`
## [1] "Chp2" "Bmp2"
##
## $`brown fat cell differentiation`
## [1] "Vstm2a" "Ptgs2" "Rgs2"
##
## $`positive regulation of epithelial cell differentiation`
## [1] "Sfn" "Bmp2" "Etv4"
##
## $`fever generation`
## [1] "Ptgs2" "Ptges"
##
## $`regulation of iron ion transport`
## [1] "Lcn2" "Hfe"
##
## $`chaperone-mediated protein folding`
## [1] "Hspb1" "Hspa8" "Hspa1a"
##
## $`regulation of odontogenesis of dentin-containing tooth`
## [1] "Wnt10a" "Bmp2"
##
## $`negative regulation of epithelial cell proliferation`
## [1] "Cav2" "Sfn" "Cdkn1c" "Etv4"
##
## $`positive regulation of cell projection organization`
## [1] "Ptprz1" "Ache" "Lcn2" "Hspb1" "Scarf1" "Rgs2"
##
## $`positive regulation of fat cell differentiation`
## [1] "Vstm2a" "Ptgs2" "Bmp2"
##
## $`response to temperature stimulus`
## [1] "Ptgs2" "Hspb1" "Hspa8" "Hspa1a"
##
## $`regulation of heat generation`
## [1] "Ptgs2" "Ptges"
##
## $`positive regulation of brown fat cell differentiation`
## [1] "Vstm2a" "Ptgs2"
##
## $`positive regulation of protein binding`
## [1] "Bambi" "Hfe" "Bmp2"
##
## $`positive regulation of nucleocytoplasmic transport`
## [1] "Ptgs2" "Chp2" "Sfn"
##
## $`negative regulation of cell adhesion`
## [1] "Ptprz1" "Hspb1" "Bcl6" "Hfe" "Bmp2"
##
## $`response to BMP`
## [1] "Vstm2a" "Bambi" "Hfe" "Bmp2"
##
## $`cellular response to BMP stimulus`
## [1] "Vstm2a" "Bambi" "Hfe" "Bmp2"
##
## $`negative regulation of smooth muscle contraction`
## [1] "Ptgs2" "Rgs2"
##
## $`regulation of cellular response to growth factor stimulus`
## [1] "Cav2" "Cdkn1c" "Bambi" "Bmp2" "Spry1"
##
## $`cellular response to chemical stress`
## [1] "Ptgs2" "Lcn2" "Fos" "Hspb1" "Hspa8"
##
## $`temperature homeostasis`
## [1] "Ptgs2" "Ache" "Lcn2" "Ptges"
##
## $`prostaglandin secretion`
## [1] "Ptgs2" "Ptges"
##
## $`learning or memory`
## [1] "Ptprz1" "Ptgs2" "Lcn2" "Fos" "Btg2"
##
## $`positive regulation by host of viral process`
## [1] "Cav2" "Hspa8"
##
## $`SMAD protein signal transduction`
## [1] "Fos" "Hfe" "Bmp2"
##
## $`lens development in camera-type eye`
## [1] "Crybb1" "Cdkn1c" "Spry1"
##
## $`regulation of odontogenesis`
## [1] "Wnt10a" "Bmp2"
##
## $`positive regulation of epidermal cell differentiation`
## [1] "Sfn" "Etv4"
##
## $`negative regulation of cyclin-dependent protein kinase activity`
## [1] "Cdk5rap1" "Cdkn1c"
##
## $`negative regulation of cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "Hfe" "Bmp2"
##
## $`regulation of phosphatase activity`
## [1] "Chp2" "Bmp2"
##
## $`regulation of insulin-like growth factor receptor signaling pathway`
## [1] "Igfbp4" "Bmp2"
##
## $`regulation of animal organ morphogenesis`
## [1] "Wnt10a" "Bmp2" "Spry1"
##
## $`positive regulation of protein localization to nucleus`
## [1] "Ptgs2" "Cav2" "Chp2"
##
## $`organ induction`
## [1] "Bmp2" "Spry1"
##
## $`skeletal muscle cell differentiation`
## [1] "Mcub" "Fos" "Btg2"
##
## $`female pregnancy`
## [1] "Ptgs2" "Fos" "Hfe" "Rgs2"
##
## $`skeletal muscle cell proliferation`
## [1] "Fos" "Cav2"
##
## $`regulation of brown fat cell differentiation`
## [1] "Vstm2a" "Ptgs2"
##
## $`regulation of cell-substrate adhesion`
## [1] "Ptprz1" "Bcl6" "Limch1" "Cspg5"
##
## $`regulation of epithelial to mesenchymal transition`
## [1] "Bambi" "Bmp2" "Spry1"
##
## $`positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cdkn1c" "Hfe" "Bmp2"
##
## $cognition
## [1] "Ptprz1" "Ptgs2" "Lcn2" "Fos" "Btg2"
##
## $`regulation of small molecule metabolic process`
## [1] "Igfbp4" "Ptgs2" "Me1" "Bmp2" "Aldob"
##
## $`cell-matrix adhesion`
## [1] "Frem1" "Bcl6" "Limch1" "Itgb8"
##
## $`positive regulation of neuron projection development`
## [1] "Ptprz1" "Hspb1" "Scarf1" "Rgs2"
##
## $`heat generation`
## [1] "Ptgs2" "Ptges"
##
## $`positive regulation of epidermis development`
## [1] "Sfn" "Etv4"
##
## $`negative regulation of muscle contraction`
## [1] "Ptgs2" "Rgs2"
##
## $`positive regulation of intracellular protein transport`
## [1] "Ptgs2" "Chp2" "Sfn"
##
## $`positive regulation of endothelial cell migration`
## [1] "Ptgs2" "Lcn2" "Hspb1"
##
## $`prostaglandin transport`
## [1] "Ptgs2" "Ptges"
##
## $`camera-type eye development`
## [1] "Ache" "Crybb1" "Fos" "Cdkn1c" "Spry1"
##
## $`prostaglandin biosynthetic process`
## [1] "Ptgs2" "Ptges"
##
## $`regulation of animal organ formation`
## [1] "Bmp2" "Spry1"
##
## $`prostanoid biosynthetic process`
## [1] "Ptgs2" "Ptges"
##
## $`cellular response to cadmium ion`
## [1] "Fos" "Hspa8"
##
## $`acute inflammatory response`
## [1] "Ptgs2" "Ptges" "Hfe"
##
## $`chaperone cofactor-dependent protein refolding`
## [1] "Hspa8" "Hspa1a"
##
## $`cardiac epithelial to mesenchymal transition`
## [1] "Bmp2" "Spry1"
##
## $`response to oxidative stress`
## [1] "Ptgs2" "Lcn2" "Fos" "Hspb1" "Hspa8"
##
## $`leukocyte cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "F11r" "Hfe" "Cd83"
##
## $`cellular response to oxidative stress`
## [1] "Lcn2" "Fos" "Hspb1" "Hspa8"
##
## $`multi-organism reproductive process`
## [1] "Ptgs2" "Fos" "Hfe" "Rgs2"
##
## $`mesenchymal cell differentiation`
## [1] "Wnt10a" "Bambi" "Bmp2" "Spry1"
##
## $`multi-multicellular organism process`
## [1] "Ptgs2" "Fos" "Hfe" "Rgs2"
##
## $`regulation of alpha-beta T cell activation`
## [1] "Bcl6" "Hfe" "Cd83"
##
## $`negative regulation of cytokine production involved in immune response`
## [1] "Bcl6" "Hfe"
##
## $`response to mechanical stimulus`
## [1] "Ptgs2" "Fos" "Btg2" "F11r"
##
## $`fat cell differentiation`
## [1] "Vstm2a" "Ptgs2" "Bmp2" "Rgs2"
##
## $`regulation of cell growth`
## [1] "Igfbp4" "Bcl6" "Sfn" "Hspa1a" "Rgs2"
##
## $`NADH metabolic process`
## [1] "Me1" "Aldob"
##
## $`regulation of dephosphorylation`
## [1] "Chp2" "Bmp2"
##
## $`mitotic nuclear division`
## [1] "Cep85" "Cav2" "Cdkn1c" "Hspa1a"
##
## $`regulation of nucleocytoplasmic transport`
## [1] "Ptgs2" "Chp2" "Sfn"
##
## $`eye development`
## [1] "Ache" "Crybb1" "Fos" "Cdkn1c" "Spry1"
##
## $`visual system development`
## [1] "Ache" "Crybb1" "Fos" "Cdkn1c" "Spry1"
##
## $`specification of animal organ identity`
## [1] "Bmp2" "Spry1"
##
## $`developmental induction`
## [1] "Bmp2" "Spry1"
##
## $`positive regulation of SMAD protein signal transduction`
## [1] "Hfe" "Bmp2"
##
## $`lens fiber cell differentiation`
## [1] "Cdkn1c" "Spry1"
##
## $`positive regulation of animal organ morphogenesis`
## [1] "Bmp2" "Spry1"
##
## $`muscle cell proliferation`
## [1] "Ptgs2" "Fos" "Cav2" "Bmp2"
##
## $`negative regulation of T cell activation`
## [1] "Hspb1" "Bcl6" "Hfe"
##
## $`sensory system development`
## [1] "Ache" "Crybb1" "Fos" "Cdkn1c" "Spry1"4.2 Type 1 Pathway Downregulated = Control ( absence of low salt)
# Arrange and filter DEGs
df <- type_1 %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers1down <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 4.01% of input gene IDs are fail to map...markers1down <- ENTREZ_list %>% inner_join(markers1down, by = "SYMBOL")
markers1down <- markers1down %>% dplyr::filter(p_val_adj < 0.05)
pos.markers1down <- markers1down %>% dplyr::filter(avg_log2FC < 0) %>% arrange(desc(abs(avg_log2FC)))
pos.ranks1down <- pos.markers1down$ENTREZID[abs(pos.markers1down$avg_log2FC) > 0.2]
# GO enrichment for downregulated genes
pos_go1down <- enrichGO(
gene = pos.ranks1down,
OrgDb = org.Mm.eg.db,
ont = "BP",
readable = TRUE
)
pos_go1down## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:104] "15395" "54156" "18703" "12309" "27528" "433229" "15925" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...13 enriched terms found
## 'data.frame': 13 obs. of 12 variables:
## $ ID : chr "GO:0097250" "GO:0045333" "GO:0015980" "GO:0009060" ...
## $ Description : chr "mitochondrial respirasome assembly" "cellular respiration" "energy derivation by oxidation of organic compounds" "aerobic respiration" ...
## $ GeneRatio : chr "6/98" "8/98" "9/98" "7/98" ...
## $ BgRatio : chr "114/28928" "271/28928" "380/28928" "206/28928" ...
## $ RichFactor : num 0.0526 0.0295 0.0237 0.034 0.0476 ...
## $ FoldEnrichment: num 15.54 8.71 6.99 10.03 14.06 ...
## $ zScore : num 9.07 7.44 6.85 7.58 7.81 ...
## $ pvalue : num 2.57e-06 4.07e-06 5.96e-06 6.71e-06 2.97e-05 ...
## $ p.adjust : num 0.00309 0.00309 0.00309 0.00309 0.01096 ...
## $ qvalue : num 0.0026 0.0026 0.0026 0.0026 0.00922 ...
## $ geneID : chr "Ndufa3/Fmc1/Pet100/Ndufb4c/Ndufa1/Ndufc1" "Ide/Ndufa3/Ndufa1/Cox6c/Ndufc1/Cs/Cox7c/Got2" "Ide/Ndufa3/Ugp2/Ndufa1/Cox6c/Ndufc1/Cs/Cox7c/Got2" "Ide/Ndufa3/Ndufa1/Cox6c/Ndufc1/Cs/Cox7c" ...
## $ Count : int 6 8 9 7 5 4 4 3 5 3 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722# Visualization
chart1down <- dotplot(pos_go1down) +
ggtitle("type 1 downregulated control") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)
) +
scale_y_discrete(
position = "right",
labels = function(x) str_wrap(x, width = 25)
)## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
4.2.1 Type 1 Down Gene View
pathway_type1down <- strsplit(pos_go1down$geneID, "/")
names(pathway_type1down) <- pos_go1down$Description
pathway_type1down## $`mitochondrial respirasome assembly`
## [1] "Ndufa3" "Fmc1" "Pet100" "Ndufb4c" "Ndufa1" "Ndufc1"
##
## $`cellular respiration`
## [1] "Ide" "Ndufa3" "Ndufa1" "Cox6c" "Ndufc1" "Cs" "Cox7c" "Got2"
##
## $`energy derivation by oxidation of organic compounds`
## [1] "Ide" "Ndufa3" "Ugp2" "Ndufa1" "Cox6c" "Ndufc1" "Cs" "Cox7c"
## [9] "Got2"
##
## $`aerobic respiration`
## [1] "Ide" "Ndufa3" "Ndufa1" "Cox6c" "Ndufc1" "Cs" "Cox7c"
##
## $`mitochondrial respiratory chain complex assembly`
## [1] "Ndufa3" "Pet100" "Ndufb4c" "Ndufa1" "Ndufc1"
##
## $`NADH dehydrogenase complex assembly`
## [1] "Ndufa3" "Ndufb4c" "Ndufa1" "Ndufc1"
##
## $`mitochondrial respiratory chain complex I assembly`
## [1] "Ndufa3" "Ndufb4c" "Ndufa1" "Ndufc1"
##
## $`activation of protein kinase B activity`
## [1] "Gas6" "Fgf1" "Ppia"
##
## $`oxidative phosphorylation`
## [1] "Ndufa3" "Ndufa1" "Cox6c" "Ndufc1" "Cox7c"
##
## $`peptidyl-proline modification`
## [1] "Fkbp11" "P3h2" "Ppia"
##
## $`regulation of body fluid levels`
## [1] "Gas6" "Apoe" "Ptger3" "Plau" "Kng1" "Ppia" "Celsr2"
##
## $`lipid droplet organization`
## [1] "Pisd" "Chka" "Ppia"
##
## $`glycerolipid metabolic process`
## [1] "Fabp5" "Apoe" "Pisd" "Chka" "Pla2g7" "Dpm3" "Abhd2"5 Type 2
5.1 Type 2 Pathway Upregulated = Low salt
df <- type_2 %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers2up <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 3.02% of input gene IDs are fail to map...markers2up <- ENTREZ_list %>% inner_join(markers2up, by = "SYMBOL")
markers2up <- markers2up %>% dplyr::filter(p_val_adj < 0.05)
#head(markers2up, n = 50)
pos.markers2up <- markers2up %>% dplyr::filter(avg_log2FC > 0) %>% arrange(desc(abs(avg_log2FC))) %>% head(200)
#change around avg log value
pos.ranks2up <- pos.markers2up$ENTREZID[abs(pos.markers2up$avg_log2FC) > 0]
#head(pos.ranks2up)
pos_go2up <- enrichGO(gene = pos.ranks2up, #a vector of entrez gene id
OrgDb = "org.Mm.eg.db",
ont = "BP",
readable = TRUE) #whether mapping gene ID to gene Name
pos_go2up## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:200] "239435" "19225" "66815" "16010" "23850" "18039" "18612" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...37 enriched terms found
## 'data.frame': 37 obs. of 12 variables:
## $ ID : chr "GO:0061077" "GO:0042026" "GO:0051085" "GO:0008217" ...
## $ Description : chr "chaperone-mediated protein folding" "protein refolding" "chaperone cofactor-dependent protein refolding" "regulation of blood pressure" ...
## $ GeneRatio : chr "7/193" "5/193" "5/193" "10/193" ...
## $ BgRatio : chr "69/28928" "24/28928" "33/28928" "229/28928" ...
## $ RichFactor : num 0.1014 0.2083 0.1515 0.0437 0.0386 ...
## $ FoldEnrichment: num 15.21 31.23 22.71 6.55 5.79 ...
## $ zScore : num 9.68 12.14 10.23 6.9 6.65 ...
## $ pvalue : num 4.01e-07 4.81e-07 2.56e-06 3.50e-06 3.73e-06 ...
## $ p.adjust : num 0.000671 0.000671 0.001621 0.001621 0.001621 ...
## $ qvalue : num 0.000562 0.000562 0.001359 0.001359 0.001359 ...
## $ geneID : chr "Hspb1/Hspa1a/Hspa1b/Clu/Tor2a/Hspa5/Hspa8" "Hspb1/Hspa1a/Hspa1b/Hspa5/Hspa8" "Hspa1a/Hspa1b/Tor2a/Hspa5/Hspa8" "Ptgs2/Ier3/Emp2/Klk1b3/F11r/Manf/Klk1/Klk1b5/Scnn1a/Gna11" ...
## $ Count : int 7 5 5 10 11 10 8 5 10 10 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722chart2up <- dotplot(pos_go2up) +
ggtitle("type 2 upregulated lowsalt") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)) +
scale_y_discrete(position = "right",
labels = function(x) str_wrap(x, width = 25)) # Wrap y-axis labels to 2 lines## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
### Gene View
pathway_type2up <- strsplit(pos_go2up$geneID, "/")
names(pathway_type2up) <- pos_go2up$Description
pathway_type2up## $`chaperone-mediated protein folding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Clu" "Tor2a" "Hspa5" "Hspa8"
##
## $`protein refolding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Hspa5" "Hspa8"
##
## $`chaperone cofactor-dependent protein refolding`
## [1] "Hspa1a" "Hspa1b" "Tor2a" "Hspa5" "Hspa8"
##
## $`regulation of blood pressure`
## [1] "Ptgs2" "Ier3" "Emp2" "Klk1b3" "F11r" "Manf" "Klk1" "Klk1b5"
## [9] "Scnn1a" "Gna11"
##
## $`protein processing`
## [1] "Klk1b3" "Immp2l" "Tysnd1" "Klk1" "Klk1b5" "Anxa2" "Mafb" "Sec11c"
## [9] "Scg5" "Ggt1" "Dhcr24"
##
## $`female pregnancy`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Emp2" "Slc2a1" "Il11ra1"
## [8] "Maged2" "Pla2g4a" "Vmp1"
##
## $`response to topologically incorrect protein`
## [1] "Hspb8" "Hspb1" "Hspa1a" "Manf" "Clu" "Eif2s1" "Hspa5" "Cops5"
##
## $`'de novo' post-translational protein folding`
## [1] "Hspa1a" "Hspa1b" "Tor2a" "Hspa5" "Hspa8"
##
## $`multi-organism reproductive process`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Emp2" "Slc2a1" "Il11ra1"
## [8] "Maged2" "Pla2g4a" "Vmp1"
##
## $`multi-multicellular organism process`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Emp2" "Slc2a1" "Il11ra1"
## [8] "Maged2" "Pla2g4a" "Vmp1"
##
## $`'de novo' protein folding`
## [1] "Hspa1a" "Hspa1b" "Tor2a" "Hspa5" "Hspa8"
##
## $`response to unfolded protein`
## [1] "Hspb8" "Hspb1" "Hspa1a" "Manf" "Eif2s1" "Hspa5" "Cops5"
##
## $`zymogen activation`
## [1] "Klk1b3" "Klk1" "Klk1b5" "Anxa2" "Ggt1" "Dhcr24"
##
## $`response to phorbol 13-acetate 12-myristate`
## [1] "Fos" "Adam15" "Btg2"
##
## $`cellular response to phorbol 13-acetate 12-myristate`
## [1] "Fos" "Adam15" "Btg2"
##
## $`protein folding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Clu" "Tor2a" "Hspa5" "Hspa8"
## [8] "Dnajb11"
##
## $`response to heat`
## [1] "Ptgs2" "Hspb1" "Hspa1a" "Hspa1b" "Eif2s1" "Hspa8"
##
## $`prostaglandin transport`
## [1] "Ptgs2" "Ptges" "Slco4a1" "Pla2g4a"
##
## $`negative regulation of apoptotic signaling pathway`
## [1] "Ptgs2" "Hspb1" "Ier3" "Hspa1b" "Clu" "Gstp1" "Pam16" "Cx3cl1"
## [9] "Lgals3"
##
## $`cellular modified amino acid metabolic process`
## [1] "Iyd" "Slco4a1" "Sardh" "Abhd12" "Gstp1" "Ggt1" "Gsta4"
## [8] "Mthfs"
##
## $decidualization
## [1] "Ptgs2" "Junb" "Il11ra1" "Pla2g4a"
##
## $`organic anion transport`
## [1] "Ptgs2" "Ptges" "Slco4a1" "Arg2" "Rgs2" "Slc2a1"
## [7] "Kcnk1" "G6pc3" "Pla2g4a" "Slc44a4" "Slc25a16" "Gipc1"
##
## $`maternal process involved in female pregnancy`
## [1] "Ptgs2" "Junb" "Rgs2" "Il11ra1" "Pla2g4a"
##
## $`plasma membrane organization`
## [1] "Mymx" "Emp2" "Anxa2" "Clu" "Mafb" "Vmp1" "Cd9"
##
## $`protein targeting`
## [1] "Immp2l" "Syngr2" "Clu" "Pam16" "Prnp" "Srp54b" "Hspa5" "Gipc1"
## [9] "Hspa8"
##
## $`regulation of apoptotic signaling pathway`
## [1] "Ptgs2" "Hspb1" "Ier3" "Hspa1b" "Clu" "Gstp1" "Pam16" "Cx3cl1"
## [9] "Maged1" "Lgals3" "Ctsc"
##
## $`maternal placenta development`
## [1] "Ptgs2" "Junb" "Il11ra1" "Pla2g4a"
##
## $`lipid transport`
## [1] "Ptgs2" "Ptges" "Slco4a1" "Prelid2" "Ttc39b" "Slc2a1" "Anxa2"
## [8] "Pitpnb" "Pla2g4a" "Vmp1" "Cd320"
##
## $`regulation of systemic arterial blood pressure`
## [1] "Ier3" "Emp2" "Klk1b3" "Manf" "Klk1" "Klk1b5"
##
## $`response to alcohol`
## [1] "Nefl" "Fos" "Pmvk" "Rgs2" "Adam15" "Btg2" "Gstp1" "Scnn1a"
## [9] "Ggt1" "Hspa8"
##
## $`protein localization to plasma membrane`
## [1] "Emp2" "F11r" "Sfn" "Anxa2" "Ramp3" "Krt18" "Prnp" "Lgals3"
## [9] "Pkdcc"
##
## $`prostaglandin secretion`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`regulation of supramolecular fiber organization`
## [1] "Capg" "Limch1" "Hspa1a" "F11r" "Hspa1b" "Clu" "Grb2" "Cx3cl1"
## [9] "Tmsb4x" "Hspa8"
##
## $`negative regulation of amide metabolic process`
## [1] "Clu" "Ormdl2" "Prnp"
##
## $`receptor recycling`
## [1] "Ache" "Anxa2" "Ramp3" "Plekhj1"
##
## $`regulation of protein kinase activity`
## [1] "Hspb1" "Cdkn1c" "Rgs2" "Emp2" "Sh3bp5" "Map2k3" "Sfn" "Gstp1"
## [9] "Prnp" "Vps25" "Maged1"
##
## $`cellular response to heat`
## [1] "Ptgs2" "Hspa1b" "Eif2s1" "Hspa8"5.2 Type 2 Pathway Downregulated = Control ( absence of low salt)
# Arrange and filter DEGs for type 2
df <- type_2 %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers2down <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 3.02% of input gene IDs are fail to map...markers2down <- ENTREZ_list %>% inner_join(markers2down, by = "SYMBOL")
markers2down <- markers2down %>% dplyr::filter(p_val_adj < 0.05)
pos.markers2down <- markers2down %>% dplyr::filter(avg_log2FC < 0) %>% arrange(desc(abs(avg_log2FC)))
pos.ranks2down <- pos.markers2down$ENTREZID[abs(pos.markers2down$avg_log2FC) > 0]
# GO enrichment for downregulated genes
pos_go2down <- enrichGO(
gene = pos.ranks2down,
OrgDb = org.Mm.eg.db,
ont = "BP",
readable = TRUE
)
pos_go2down## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:21] "54156" "15925" "54608" "72514" "19218" "14180" "20503" "18792" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...10 enriched terms found
## 'data.frame': 10 obs. of 12 variables:
## $ ID : chr "GO:0014910" "GO:0044344" "GO:0071774" "GO:0014909" ...
## $ Description : chr "regulation of smooth muscle cell migration" "cellular response to fibroblast growth factor stimulus" "response to fibroblast growth factor" "smooth muscle cell migration" ...
## $ GeneRatio : chr "3/21" "3/21" "3/21" "3/21" ...
## $ BgRatio : chr "110/28928" "111/28928" "118/28928" "122/28928" ...
## $ RichFactor : num 0.0273 0.027 0.0254 0.0246 0.0217 ...
## $ FoldEnrichment: num 37.6 37.2 35 33.9 29.9 ...
## $ zScore : num 10.36 10.31 9.98 9.81 9.19 ...
## $ pvalue : num 6.77e-05 6.95e-05 8.34e-05 9.21e-05 1.33e-04 ...
## $ p.adjust : num 0.0194 0.0194 0.0194 0.0194 0.0223 ...
## $ qvalue : num 0.0119 0.0119 0.0119 0.0119 0.0138 ...
## $ geneID : chr "Abhd2/Fgf9/Plau" "Fgfbp3/Fgf9/Zfp36l1" "Fgfbp3/Fgf9/Zfp36l1" "Abhd2/Fgf9/Plau" ...
## $ Count : int 3 3 3 3 3 3 2 3 3 3
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722# Visualization
chart2down <- dotplot(pos_go2down) +
ggtitle("type 2 downregulated control") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)
) +
scale_y_discrete(
position = "right",
labels = function(x) str_wrap(x, width = 25)
)## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
5.2.1 Gene View
pathway_type2down <- strsplit(pos_go2down$geneID, "/")
names(pathway_type2down) <- pos_go2down$Description
pathway_type2down## $`regulation of smooth muscle cell migration`
## [1] "Abhd2" "Fgf9" "Plau"
##
## $`cellular response to fibroblast growth factor stimulus`
## [1] "Fgfbp3" "Fgf9" "Zfp36l1"
##
## $`response to fibroblast growth factor`
## [1] "Fgfbp3" "Fgf9" "Zfp36l1"
##
## $`smooth muscle cell migration`
## [1] "Abhd2" "Fgf9" "Plau"
##
## $`muscle cell migration`
## [1] "Abhd2" "Fgf9" "Plau"
##
## $`regulation of mRNA processing`
## [1] "Zfp36l1" "Alkbh5" "Rbm47"
##
## $`norepinephrine transport`
## [1] "Ptger3" "Actb"
##
## $`regulation of mRNA stability`
## [1] "Zfp36l1" "Alkbh5" "Rbm47"
##
## $`regulation of RNA stability`
## [1] "Zfp36l1" "Alkbh5" "Rbm47"
##
## $`regulation of mRNA catabolic process`
## [1] "Zfp36l1" "Alkbh5" "Rbm47"6 Type 3 Upregulated -> lowsalt
# Arrange and filter DEGs for type 3
df <- type_3 %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers3up <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 21.05% of input gene IDs are fail to map...markers3up <- ENTREZ_list %>% inner_join(markers3up, by = "SYMBOL")
markers3up <- markers3up %>% dplyr::filter(p_val_adj < 0.05)
#head(markers3up, n = 50)
pos.markers3up <- markers3up %>% dplyr::filter(avg_log2FC > 0) %>% arrange(desc(abs(avg_log2FC)))
#change around avg log value
pos.ranks3up <- pos.markers3up$ENTREZID[abs(pos.markers3up$avg_log2FC) > 0]
#head(pos.ranks3up)
pos_go3up <- enrichGO(
gene = pos.ranks3up, # a vector of entrez gene id
OrgDb = org.Mm.eg.db,
ont = "BP",
readable = TRUE # whether mapping gene ID to gene Name
)
pos_go3up## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:7] "102436" "100040531" "232341" "56455" "16372" "80733" "20377"
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...223 enriched terms found
## 'data.frame': 223 obs. of 12 variables:
## $ ID : chr "GO:0090263" "GO:0035282" "GO:0030177" "GO:0001838" ...
## $ Description : chr "positive regulation of canonical Wnt signaling pathway" "segmentation" "positive regulation of Wnt signaling pathway" "embryonic epithelial tube formation" ...
## $ GeneRatio : chr "2/7" "2/7" "2/7" "2/7" ...
## $ BgRatio : chr "110/28928" "118/28928" "145/28928" "154/28928" ...
## $ RichFactor : num 0.0182 0.0169 0.0138 0.013 0.012 ...
## $ FoldEnrichment: num 75.1 70 57 53.7 49.5 ...
## $ zScore : num 12.12 11.69 10.52 10.2 9.78 ...
## $ pvalue : num 0.000297 0.000342 0.000515 0.000581 0.000683 ...
## $ p.adjust : num 0.0301 0.0301 0.0301 0.0301 0.0301 ...
## $ qvalue : num 0.00846 0.00846 0.00846 0.00846 0.00846 ...
## $ geneID : chr "Wnk1/Sfrp1" "Irx2/Sfrp1" "Wnk1/Sfrp1" "Irx2/Sfrp1" ...
## $ Count : int 2 2 2 2 2 2 2 2 2 2 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722chart3up <- dotplot(pos_go3up) +
ggtitle("type 3 upregulated lowsalt") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)
) +
scale_y_discrete(
position = "right",
labels = function(x) str_wrap(x, width = 25)
) # Wrap y-axis labels to 2 lines## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
6.1 Gene View Upregulated Type 3
pathway_type3up <- strsplit(pos_go3up$geneID, "/")
names(pathway_type3up) <- pos_go3up$Description
pathway_type3up## $`positive regulation of canonical Wnt signaling pathway`
## [1] "Wnk1" "Sfrp1"
##
## $segmentation
## [1] "Irx2" "Sfrp1"
##
## $`positive regulation of Wnt signaling pathway`
## [1] "Wnk1" "Sfrp1"
##
## $`embryonic epithelial tube formation`
## [1] "Irx2" "Sfrp1"
##
## $`epithelial tube formation`
## [1] "Irx2" "Sfrp1"
##
## $`kidney epithelium development`
## [1] "Irx2" "Sfrp1"
##
## $`tube formation`
## [1] "Irx2" "Sfrp1"
##
## $`morphogenesis of embryonic epithelium`
## [1] "Irx2" "Sfrp1"
##
## $gastrulation
## [1] "Wnk1" "Sfrp1"
##
## $`negative regulation of secretion`
## [1] "Wnk1" "Sfrp1"
##
## $`regulation of insulin secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`negative regulation of protein localization`
## [1] "Wnk1" "Sfrp1"
##
## $`regulation of canonical Wnt signaling pathway`
## [1] "Wnk1" "Sfrp1"
##
## $`insulin secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`regulation of peptide hormone secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`regulation of peptide secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`regulation of peptide transport`
## [1] "Dynll1" "Sfrp1"
##
## $`canonical Wnt signaling pathway`
## [1] "Wnk1" "Sfrp1"
##
## $`regulation by virus of viral protein levels in host cell`
## [1] "Dynlt1f"
##
## $`DNA strand resection involved in replication fork processing`
## [1] "Dynll1"
##
## $`regulation of Wnt signaling pathway`
## [1] "Wnk1" "Sfrp1"
##
## $`peptide hormone secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`negative regulation of cell adhesion mediated by integrin`
## [1] "Wnk1"
##
## $`negative regulation of heterotypic cell-cell adhesion`
## [1] "Wnk1"
##
## $`protein insertion into ER membrane by stop-transfer membrane-anchor sequence`
## [1] "Wnk1"
##
## $`regulation of cell-cell adhesion involved in gastrulation`
## [1] "Wnk1"
##
## $`cellular response to X-ray`
## [1] "Sfrp1"
##
## $`regulation of dopaminergic neuron differentiation`
## [1] "Sfrp1"
##
## $`regulation of ribonucleoprotein complex localization`
## [1] "Wnk1"
##
## $`negative regulation of phosphorylation`
## [1] "Dynll1" "Sfrp1"
##
## $`peptide secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`regulation of protein secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`regulation of cell-cell adhesion mediated by integrin`
## [1] "Wnk1"
##
## $`prostate glandular acinus development`
## [1] "Sfrp1"
##
## $`cell-cell adhesion involved in gastrulation`
## [1] "Wnk1"
##
## $`ribonucleoprotein complex localization`
## [1] "Wnk1"
##
## $`loop of Henle development`
## [1] "Irx2"
##
## $`aminoacyl-tRNA metabolism involved in translational fidelity`
## [1] "Lars2"
##
## $`positive regulation of non-motile cilium assembly`
## [1] "Dynll1"
##
## $`regulation of hormone secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`peptide transport`
## [1] "Dynll1" "Sfrp1"
##
## $`dorsal/ventral axis specification`
## [1] "Sfrp1"
##
## $`negative regulation of osteoblast proliferation`
## [1] "Sfrp1"
##
## $`positive regulation of mitotic cytokinesis`
## [1] "Wnk1"
##
## $`positive regulation of fibroblast apoptotic process`
## [1] "Sfrp1"
##
## $`kidney development`
## [1] "Irx2" "Sfrp1"
##
## $`positive regulation of T cell chemotaxis`
## [1] "Wnk1"
##
## $`bone trabecula formation`
## [1] "Sfrp1"
##
## $`positive regulation of extrinsic apoptotic signaling pathway via death domain receptors`
## [1] "Sfrp1"
##
## $`midbrain dopaminergic neuron differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of phosphorus metabolic process`
## [1] "Dynll1" "Sfrp1"
##
## $`negative regulation of phosphate metabolic process`
## [1] "Dynll1" "Sfrp1"
##
## $`regulation of T cell chemotaxis`
## [1] "Wnk1"
##
## $`neural crest formation`
## [1] "Sfrp1"
##
## $`pancreatic juice secretion`
## [1] "Wnk1"
##
## $`branching involved in prostate gland morphogenesis`
## [1] "Sfrp1"
##
## $`cellular response to prostaglandin E stimulus`
## [1] "Sfrp1"
##
## $`regulation of mitotic cytokinesis`
## [1] "Wnk1"
##
## $`renal system development`
## [1] "Irx2" "Sfrp1"
##
## $`cellular response to abiotic stimulus`
## [1] "Wnk1" "Sfrp1"
##
## $`cellular response to environmental stimulus`
## [1] "Wnk1" "Sfrp1"
##
## $`negative regulation of sodium ion transport`
## [1] "Wnk1"
##
## $`intracellular chloride ion homeostasis`
## [1] "Wnk1"
##
## $`intraciliary retrograde transport`
## [1] "Dynll1"
##
## $`negative regulation of JUN kinase activity`
## [1] "Sfrp1"
##
## $`regulation of RNA export from nucleus`
## [1] "Wnk1"
##
## $`regulation of non-motile cilium assembly`
## [1] "Dynll1"
##
## $`positive regulation of non-canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`epithelial tube morphogenesis`
## [1] "Irx2" "Sfrp1"
##
## $`amide transport`
## [1] "Dynll1" "Sfrp1"
##
## $`regulation of translational fidelity`
## [1] "Lars2"
##
## $`intracellular monoatomic anion homeostasis`
## [1] "Wnk1"
##
## $`hormone secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`negative regulation of protein modification process`
## [1] "Wnk1" "Sfrp1"
##
## $`hormone transport`
## [1] "Dynll1" "Sfrp1"
##
## $`convergent extension`
## [1] "Sfrp1"
##
## $`negative regulation of androgen receptor signaling pathway`
## [1] "Sfrp1"
##
## $`bone trabecula morphogenesis`
## [1] "Sfrp1"
##
## $`regulation of nucleobase-containing compound transport`
## [1] "Wnk1"
##
## $`positive regulation of Rac protein signal transduction`
## [1] "Dynlt1f"
##
## $`negative regulation of nitric oxide biosynthetic process`
## [1] "Dynll1"
##
## $`cellular response to prostaglandin stimulus`
## [1] "Sfrp1"
##
## $`positive regulation of lymphocyte chemotaxis`
## [1] "Wnk1"
##
## $`negative regulation of nitric oxide metabolic process`
## [1] "Dynll1"
##
## $`protein secretion`
## [1] "Dynll1" "Sfrp1"
##
## $`establishment of protein localization to extracellular region`
## [1] "Dynll1" "Sfrp1"
##
## $`cell-cell adhesion mediated by integrin`
## [1] "Wnk1"
##
## $`negative regulation of bone remodeling`
## [1] "Sfrp1"
##
## $`negative regulation of digestive system process`
## [1] "Wnk1"
##
## $`regulation of type B pancreatic cell proliferation`
## [1] "Sfrp1"
##
## $`protein localization to extracellular region`
## [1] "Dynll1" "Sfrp1"
##
## $regionalization
## [1] "Irx2" "Sfrp1"
##
## $`segment specification`
## [1] "Irx2"
##
## $`negative regulation of DNA replication`
## [1] "Dynll1"
##
## $`negative regulation of mitochondrial membrane permeability`
## [1] "Dynlt1f"
##
## $`Wnt signaling pathway`
## [1] "Wnk1" "Sfrp1"
##
## $`positive regulation of cell projection organization`
## [1] "Dynlt1f" "Dynll1"
##
## $`cellular response to vitamin D`
## [1] "Sfrp1"
##
## $`nephron tubule formation`
## [1] "Irx2"
##
## $`negative regulation of membrane permeability`
## [1] "Dynlt1f"
##
## $`T cell chemotaxis`
## [1] "Wnk1"
##
## $`regulation of heterotypic cell-cell adhesion`
## [1] "Wnk1"
##
## $`negative regulation of GTPase activity`
## [1] "Wnk1"
##
## $`regulation of lymphocyte chemotaxis`
## [1] "Wnk1"
##
## $`regulation of fibroblast apoptotic process`
## [1] "Sfrp1"
##
## $`DNA-templated transcription termination`
## [1] "Wnk1"
##
## $`chloride ion homeostasis`
## [1] "Wnk1"
##
## $`positive regulation of systemic arterial blood pressure`
## [1] "Wnk1"
##
## $`response to X-ray`
## [1] "Sfrp1"
##
## $`negative regulation of tissue remodeling`
## [1] "Sfrp1"
##
## $`mitochondrion distribution`
## [1] "Dynll1"
##
## $`monoatomic anion homeostasis`
## [1] "Wnk1"
##
## $`regulation of androgen receptor signaling pathway`
## [1] "Sfrp1"
##
## $`regulation of non-canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`fibroblast apoptotic process`
## [1] "Sfrp1"
##
## $`protein insertion into ER membrane`
## [1] "Wnk1"
##
## $`trabecula formation`
## [1] "Sfrp1"
##
## $`cellular response to vitamin`
## [1] "Sfrp1"
##
## $`regulation of osteoblast proliferation`
## [1] "Sfrp1"
##
## $`negative regulation of protein localization to plasma membrane`
## [1] "Wnk1"
##
## $`Wnt signaling pathway, planar cell polarity pathway`
## [1] "Sfrp1"
##
## $`positive regulation of cilium assembly`
## [1] "Dynll1"
##
## $`prostate gland epithelium morphogenesis`
## [1] "Sfrp1"
##
## $`negative regulation of protein localization to cell periphery`
## [1] "Wnk1"
##
## $`regulation of Rac protein signal transduction`
## [1] "Dynlt1f"
##
## $`prostate gland morphogenesis`
## [1] "Sfrp1"
##
## $`cellular hyperosmotic response`
## [1] "Wnk1"
##
## $`establishment of mitochondrion localization`
## [1] "Dynll1"
##
## $`potassium ion homeostasis`
## [1] "Wnk1"
##
## $`axis elongation`
## [1] "Sfrp1"
##
## $`response to vitamin D`
## [1] "Sfrp1"
##
## $`response to prostaglandin E`
## [1] "Sfrp1"
##
## $`negative regulation of B cell activation`
## [1] "Sfrp1"
##
## $`proximal/distal pattern formation`
## [1] "Irx2"
##
## $`osteoblast proliferation`
## [1] "Sfrp1"
##
## $`cellular response to estradiol stimulus`
## [1] "Sfrp1"
##
## $`positive regulation of potassium ion transmembrane transport`
## [1] "Wnk1"
##
## $`positive regulation of T cell migration`
## [1] "Wnk1"
##
## $`establishment of planar polarity`
## [1] "Sfrp1"
##
## $`establishment of tissue polarity`
## [1] "Sfrp1"
##
## $`type B pancreatic cell proliferation`
## [1] "Sfrp1"
##
## $`regulation of B cell differentiation`
## [1] "Sfrp1"
##
## $`cell volume homeostasis`
## [1] "Wnk1"
##
## $`negative regulation of epithelial to mesenchymal transition`
## [1] "Sfrp1"
##
## $`positive regulation of protein-containing complex disassembly`
## [1] "Wnk1"
##
## $`negative regulation of JNK cascade`
## [1] "Sfrp1"
##
## $`tRNA aminoacylation for protein translation`
## [1] "Lars2"
##
## $`hyperosmotic response`
## [1] "Wnk1"
##
## $`negative regulation of osteoclast differentiation`
## [1] "Sfrp1"
##
## $`cellular response to estrogen stimulus`
## [1] "Sfrp1"
##
## $`negative regulation of protein localization to membrane`
## [1] "Wnk1"
##
## $`one-carbon metabolic process`
## [1] "Car15"
##
## $`negative regulation of intracellular steroid hormone receptor signaling pathway`
## [1] "Sfrp1"
##
## $`lymphocyte chemotaxis`
## [1] "Wnk1"
##
## $`response to prostaglandin`
## [1] "Sfrp1"
##
## $`metanephric nephron development`
## [1] "Irx2"
##
## $`regulation of DNA-templated DNA replication`
## [1] "Dynll1"
##
## $`tRNA aminoacylation`
## [1] "Lars2"
##
## $`positive regulation of smoothened signaling pathway`
## [1] "Sfrp1"
##
## $`positive regulation of lymphocyte migration`
## [1] "Wnk1"
##
## $`amino acid activation`
## [1] "Lars2"
##
## $`hematopoietic stem cell differentiation`
## [1] "Sfrp1"
##
## $`positive regulation of cytokinesis`
## [1] "Wnk1"
##
## $`negative regulation of fibroblast proliferation`
## [1] "Sfrp1"
##
## $`negative regulation of ossification`
## [1] "Sfrp1"
##
## $`androgen receptor signaling pathway`
## [1] "Sfrp1"
##
## $`positive regulation of potassium ion transport`
## [1] "Wnk1"
##
## $`protein insertion into membrane`
## [1] "Wnk1"
##
## $`dopaminergic neuron differentiation`
## [1] "Sfrp1"
##
## $`potassium ion import across plasma membrane`
## [1] "Wnk1"
##
## $`regulation of extrinsic apoptotic signaling pathway via death domain receptors`
## [1] "Sfrp1"
##
## $`midbrain development`
## [1] "Sfrp1"
##
## $`replication fork processing`
## [1] "Dynll1"
##
## $`positive regulation of insulin secretion involved in cellular response to glucose stimulus`
## [1] "Dynll1"
##
## $`regulation of cell adhesion mediated by integrin`
## [1] "Wnk1"
##
## $`negative regulation of peptidyl-tyrosine phosphorylation`
## [1] "Sfrp1"
##
## $`regulation of T cell migration`
## [1] "Wnk1"
##
## $`cellular response to nutrient`
## [1] "Sfrp1"
##
## $`negative regulation of MAP kinase activity`
## [1] "Sfrp1"
##
## $`regulation of digestive system process`
## [1] "Wnk1"
##
## $`intraciliary transport`
## [1] "Dynll1"
##
## $`trabecula morphogenesis`
## [1] "Sfrp1"
##
## $`DNA-templated DNA replication maintenance of fidelity`
## [1] "Dynll1"
##
## $`digestive tract morphogenesis`
## [1] "Sfrp1"
##
## $`secretion by tissue`
## [1] "Wnk1"
##
## $`Rac protein signal transduction`
## [1] "Dynlt1f"
##
## $`positive regulation of blood pressure`
## [1] "Wnk1"
##
## $`regulation of mitochondrial membrane permeability`
## [1] "Dynlt1f"
##
## $`mitochondrion localization`
## [1] "Dynll1"
##
## $`regulation of sodium ion transmembrane transport`
## [1] "Wnk1"
##
## $`prostate gland development`
## [1] "Sfrp1"
##
## $`negative regulation of BMP signaling pathway`
## [1] "Sfrp1"
##
## $`heterotypic cell-cell adhesion`
## [1] "Wnk1"
##
## $`non-canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`morphogenesis of a polarized epithelium`
## [1] "Sfrp1"
##
## $`negative regulation of myeloid leukocyte differentiation`
## [1] "Sfrp1"
##
## $`regulation of bone remodeling`
## [1] "Sfrp1"
##
## $`regulation of JUN kinase activity`
## [1] "Sfrp1"
##
## $`negative regulation of lymphocyte differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of insulin secretion`
## [1] "Sfrp1"
##
## $`regulation of morphogenesis of a branching structure`
## [1] "Sfrp1"
##
## $`positive regulation of extrinsic apoptotic signaling pathway`
## [1] "Sfrp1"
##
## $`regulation of lymphocyte migration`
## [1] "Wnk1"
##
## $`positive regulation of fat cell differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of osteoblast differentiation`
## [1] "Sfrp1"
##
## $`T cell migration`
## [1] "Wnk1"
##
## $`mRNA export from nucleus`
## [1] "Wnk1"
##
## $`regulation of morphogenesis of an epithelium`
## [1] "Sfrp1"
##
## $`non-motile cilium assembly`
## [1] "Dynll1"
##
## $`urogenital system development`
## [1] "Sfrp1"
##
## $somitogenesis
## [1] "Sfrp1"
##
## $`cardiac muscle cell apoptotic process`
## [1] "Dynlt1f"
##
## $`regulation of membrane permeability`
## [1] "Dynlt1f"
##
## $`regulation of nitric oxide biosynthetic process`
## [1] "Dynll1"
##
## $`negative regulation of peptide hormone secretion`
## [1] "Sfrp1"
##
## $`striated muscle cell apoptotic process`
## [1] "Dynlt1f"
##
## $`positive regulation of small GTPase mediated signal transduction`
## [1] "Dynlt1f"
##
## $`cellular response to osmotic stress`
## [1] "Wnk1"
##
## $`negative regulation of peptide secretion`
## [1] "Sfrp1"
##
## $`regulation of cilium assembly`
## [1] "Dynll1"
##
## $`regulation of nitric oxide metabolic process`
## [1] "Dynll1"
##
## $`regulation of intracellular steroid hormone receptor signaling pathway`
## [1] "Sfrp1"
##
## $`cellular response to interleukin-1`
## [1] "Sfrp1"6.2 Type 3 Downregulated Control asbence of low salt
# Arrange and filter DEGs for type 3
df <- type_3 %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df
markers3down <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 2.03% of input gene IDs are fail to map...markers3down <- ENTREZ_list %>% inner_join(markers3down, by = "SYMBOL")
markers3down <- markers3down %>% dplyr::filter(p_val_adj < 0.05)
#head(markers3down, n = 50)
pos.markers3down <- markers3down %>% dplyr::filter(avg_log2FC < 0) %>% arrange(desc(abs(avg_log2FC)))
# You can adjust the log2FC threshold here if you want a stricter cutoff
pos.ranks3down <- pos.markers3down$ENTREZID[abs(pos.markers3down$avg_log2FC) > 0]
#head(pos.ranks3down)
pos_go3down <- enrichGO(
gene = pos.ranks3down, # a vector of entrez gene id
OrgDb = org.Mm.eg.db,
ont = "BP",
readable = TRUE # whether mapping gene ID to gene Name
)
pos_go3down## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:8] "13653" "11461" "54405" "378702" "66091" "17992" "12864" "12868"
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...98 enriched terms found
## 'data.frame': 98 obs. of 12 variables:
## $ ID : chr "GO:0006119" "GO:0009060" "GO:0045333" "GO:0015980" ...
## $ Description : chr "oxidative phosphorylation" "aerobic respiration" "cellular respiration" "energy derivation by oxidation of organic compounds" ...
## $ GeneRatio : chr "4/8" "4/8" "4/8" "4/8" ...
## $ BgRatio : chr "154/28928" "206/28928" "271/28928" "380/28928" ...
## $ RichFactor : num 0.026 0.0194 0.0148 0.0105 0.0308 ...
## $ FoldEnrichment: num 93.9 70.2 53.4 38.1 111.3 ...
## $ zScore : num 19.2 16.6 14.4 12.1 14.8 ...
## $ pvalue : num 5.32e-08 1.71e-07 5.12e-07 1.97e-06 1.38e-04 ...
## $ p.adjust : num 1.56e-05 2.51e-05 5.02e-05 1.45e-04 6.16e-03 ...
## $ qvalue : num 5.88e-06 9.45e-06 1.89e-05 5.44e-05 2.32e-03 ...
## $ geneID : chr "Ndufa1/Ndufa3/Cox6c/Cox8a" "Ndufa1/Ndufa3/Cox6c/Cox8a" "Ndufa1/Ndufa3/Cox6c/Cox8a" "Ndufa1/Ndufa3/Cox6c/Cox8a" ...
## $ Count : int 4 4 4 4 2 2 2 2 2 2 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722chart3down <- dotplot(pos_go3down) +
ggtitle("type 3 downregulated lowsalt") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)
) +
scale_y_discrete(
position = "right",
labels = function(x) str_wrap(x, width = 25)
) # Wrap y-axis labels to 2 lines## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
6.3 Gene View Down regulated
pathway_type3down <- strsplit(pos_go3down$geneID, "/")
names(pathway_type3down) <- pos_go3down$Description
pathway_type3down## $`oxidative phosphorylation`
## [1] "Ndufa1" "Ndufa3" "Cox6c" "Cox8a"
##
## $`aerobic respiration`
## [1] "Ndufa1" "Ndufa3" "Cox6c" "Cox8a"
##
## $`cellular respiration`
## [1] "Ndufa1" "Ndufa3" "Cox6c" "Cox8a"
##
## $`energy derivation by oxidation of organic compounds`
## [1] "Ndufa1" "Ndufa3" "Cox6c" "Cox8a"
##
## $`NADH dehydrogenase complex assembly`
## [1] "Ndufa1" "Ndufa3"
##
## $`mitochondrial respiratory chain complex I assembly`
## [1] "Ndufa1" "Ndufa3"
##
## $`proton motive force-driven mitochondrial ATP synthesis`
## [1] "Ndufa1" "Ndufa3"
##
## $`proton motive force-driven ATP synthesis`
## [1] "Ndufa1" "Ndufa3"
##
## $`ATP biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`mitochondrial respiratory chain complex assembly`
## [1] "Ndufa1" "Ndufa3"
##
## $`purine ribonucleoside triphosphate biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`mitochondrial respirasome assembly`
## [1] "Ndufa1" "Ndufa3"
##
## $`purine nucleoside triphosphate biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`ribonucleoside triphosphate biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`nucleoside triphosphate biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`purine ribonucleotide biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`ribonucleotide biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`ribose phosphate biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`purine nucleotide biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`regulation of transmembrane transporter activity`
## [1] "Actb" "Ndufa4"
##
## $`regulation of transporter activity`
## [1] "Actb" "Ndufa4"
##
## $`nucleotide biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`ATP metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`purine-containing compound biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`purine ribonucleoside triphosphate metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`ribonucleoside triphosphate metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`purine nucleoside triphosphate metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`positive regulation of cell proliferation involved in kidney development`
## [1] "Egr1"
##
## $`nucleoside triphosphate metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`positive regulation of gene expression via chromosomal CpG island demethylation`
## [1] "Egr1"
##
## $`cell proliferation involved in metanephros development`
## [1] "Egr1"
##
## $`nucleoside phosphate biosynthetic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`regulation of glomerular mesangial cell proliferation`
## [1] "Egr1"
##
## $`adherens junction assembly`
## [1] "Actb"
##
## $`glomerular mesangial cell proliferation`
## [1] "Egr1"
##
## $`T cell differentiation`
## [1] "Egr1" "Actb"
##
## $`positive regulation of hormone biosynthetic process`
## [1] "Egr1"
##
## $`cellular response to electrical stimulus`
## [1] "Actb"
##
## $`apical protein localization`
## [1] "Actb"
##
## $`purine ribonucleotide metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`regulation of cell proliferation involved in kidney development`
## [1] "Egr1"
##
## $`ribonucleotide metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`estrous cycle`
## [1] "Egr1"
##
## $`metanephric glomerulus development`
## [1] "Egr1"
##
## $`ribose phosphate metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`glomerular mesangium development`
## [1] "Egr1"
##
## $`catecholamine uptake`
## [1] "Actb"
##
## $`cellular response to abiotic stimulus`
## [1] "Egr1" "Actb"
##
## $`cellular response to environmental stimulus`
## [1] "Egr1" "Actb"
##
## $`mitochondrial electron transport, cytochrome c to oxygen`
## [1] "Cox8a"
##
## $`progesterone metabolic process`
## [1] "Egr1"
##
## $`C21-steroid hormone biosynthetic process`
## [1] "Egr1"
##
## $`regulation of ketone biosynthetic process`
## [1] "Egr1"
##
## $`cell proliferation involved in kidney development`
## [1] "Egr1"
##
## $`purine nucleotide metabolic process`
## [1] "Ndufa1" "Ndufa3"
##
## $`postsynaptic actin cytoskeleton organization`
## [1] "Actb"
##
## $`negative regulation of cyclin-dependent protein kinase activity`
## [1] "Actb"
##
## $`regulation of proton transport`
## [1] "Ndufa4"
##
## $`positive regulation of hormone metabolic process`
## [1] "Egr1"
##
## $`lymphocyte differentiation`
## [1] "Egr1" "Actb"
##
## $`regulation of protein sumoylation`
## [1] "Egr1"
##
## $`protein localization to cell-cell junction`
## [1] "Actb"
##
## $`interleukin-1-mediated signaling pathway`
## [1] "Egr1"
##
## $`regulation of nucleotide-excision repair`
## [1] "Actb"
##
## $`locomotor rhythm`
## [1] "Egr1"
##
## $`cellular response to gamma radiation`
## [1] "Egr1"
##
## $`postsynaptic cytoskeleton organization`
## [1] "Actb"
##
## $`regulation of hormone biosynthetic process`
## [1] "Egr1"
##
## $`glomerulus vasculature development`
## [1] "Egr1"
##
## $`olefinic compound biosynthetic process`
## [1] "Egr1"
##
## $`norepinephrine transport`
## [1] "Actb"
##
## $`renal system vasculature development`
## [1] "Egr1"
##
## $`kidney vasculature development`
## [1] "Egr1"
##
## $`regulation of synaptic vesicle endocytosis`
## [1] "Actb"
##
## $`regulation of G0 to G1 transition`
## [1] "Actb"
##
## $`positive regulation of oxidoreductase activity`
## [1] "Ndufa4"
##
## $`transepithelial transport`
## [1] "Actb"
##
## $`G0 to G1 transition`
## [1] "Actb"
##
## $`regulation of long-term neuronal synaptic plasticity`
## [1] "Egr1"
##
## $`regulation of synaptic vesicle recycling`
## [1] "Actb"
##
## $`metanephric nephron development`
## [1] "Egr1"
##
## $`positive regulation of double-strand break repair via homologous recombination`
## [1] "Actb"
##
## $`steroid hormone biosynthetic process`
## [1] "Egr1"
##
## $`C21-steroid hormone metabolic process`
## [1] "Egr1"
##
## $`long-term memory`
## [1] "Egr1"
##
## $`protein sumoylation`
## [1] "Egr1"
##
## $`positive regulation of stem cell population maintenance`
## [1] "Actb"
##
## $`ketone biosynthetic process`
## [1] "Egr1"
##
## $`positive regulation of myoblast differentiation`
## [1] "Actb"
##
## $`regulation of cyclin-dependent protein kinase activity`
## [1] "Actb"
##
## $`regulation of hormone metabolic process`
## [1] "Egr1"
##
## $`response to electrical stimulus`
## [1] "Actb"
##
## $`response to gamma radiation`
## [1] "Egr1"
##
## $`transcription initiation-coupled chromatin remodeling`
## [1] "Egr1"
##
## $`positive regulation of miRNA transcription`
## [1] "Egr1"
##
## $`protein destabilization`
## [1] "Serf2"
##
## $`adherens junction organization`
## [1] "Actb"
##
## $`positive regulation of gene expression, epigenetic`
## [1] "Egr1"7 Type 4
7.1 Type 4 Upregulated lowsalt
# Arrange and filter DEGs for type 4
df <- type_4 %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers4up <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columnsmarkers4up <- ENTREZ_list %>% inner_join(markers4up, by = "SYMBOL")
markers4up <- markers4up %>% dplyr::filter(p_val_adj < 0.05)
#head(markers4up, n = 50)
pos.markers4up <- markers4up %>% dplyr::filter(avg_log2FC > 0) %>% arrange(desc(abs(avg_log2FC)))
# Adjust avg_log2FC threshold as needed
pos.ranks4up <- pos.markers4up$ENTREZID[abs(pos.markers4up$avg_log2FC) > 0]
#head(pos.ranks4up)
pos_go4up <- enrichGO(
gene = pos.ranks4up, # a vector of entrez gene id
OrgDb = org.Mm.eg.db,
ont = "BP",
readable = TRUE # whether mapping gene ID to gene Name
)
pos_go4up## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr "20377"
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...285 enriched terms found
## 'data.frame': 285 obs. of 12 variables:
## $ ID : chr "GO:0071481" "GO:1904338" "GO:0060525" "GO:0009950" ...
## $ Description : chr "cellular response to X-ray" "regulation of dopaminergic neuron differentiation" "prostate glandular acinus development" "dorsal/ventral axis specification" ...
## $ GeneRatio : chr "1/1" "1/1" "1/1" "1/1" ...
## $ BgRatio : chr "11/28928" "11/28928" "12/28928" "13/28928" ...
## $ RichFactor : num 0.0909 0.0909 0.0833 0.0769 0.0769 ...
## $ FoldEnrichment: num 2630 2630 2411 2225 2225 ...
## $ zScore : num 51.3 51.3 49.1 47.2 47.2 ...
## $ pvalue : num 0.00038 0.00038 0.000415 0.000449 0.000449 ...
## $ p.adjust : num 0.00842 0.00842 0.00842 0.00842 0.00842 ...
## $ qvalue : logi NA NA NA NA NA NA ...
## $ geneID : chr "Sfrp1" "Sfrp1" "Sfrp1" "Sfrp1" ...
## $ Count : int 1 1 1 1 1 1 1 1 1 1 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722chart4up <- dotplot(pos_go4up) +
ggtitle("type 4 upregulated lowsalt") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)
) +
scale_y_discrete(
position = "right",
labels = function(x) str_wrap(x, width = 25)
) # Wrap y-axis labels to 2 lines## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
7.2 Gene View Upregulated
pathway_type4up <- strsplit(pos_go4up$geneID, "/")
names(pathway_type4up) <- pos_go4up$Description
pathway_type4up## $`cellular response to X-ray`
## [1] "Sfrp1"
##
## $`regulation of dopaminergic neuron differentiation`
## [1] "Sfrp1"
##
## $`prostate glandular acinus development`
## [1] "Sfrp1"
##
## $`dorsal/ventral axis specification`
## [1] "Sfrp1"
##
## $`negative regulation of osteoblast proliferation`
## [1] "Sfrp1"
##
## $`positive regulation of fibroblast apoptotic process`
## [1] "Sfrp1"
##
## $`bone trabecula formation`
## [1] "Sfrp1"
##
## $`positive regulation of extrinsic apoptotic signaling pathway via death domain receptors`
## [1] "Sfrp1"
##
## $`midbrain dopaminergic neuron differentiation`
## [1] "Sfrp1"
##
## $`neural crest formation`
## [1] "Sfrp1"
##
## $`branching involved in prostate gland morphogenesis`
## [1] "Sfrp1"
##
## $`cellular response to prostaglandin E stimulus`
## [1] "Sfrp1"
##
## $`negative regulation of JUN kinase activity`
## [1] "Sfrp1"
##
## $`positive regulation of non-canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`convergent extension`
## [1] "Sfrp1"
##
## $`negative regulation of androgen receptor signaling pathway`
## [1] "Sfrp1"
##
## $`bone trabecula morphogenesis`
## [1] "Sfrp1"
##
## $`cellular response to prostaglandin stimulus`
## [1] "Sfrp1"
##
## $`negative regulation of bone remodeling`
## [1] "Sfrp1"
##
## $`regulation of type B pancreatic cell proliferation`
## [1] "Sfrp1"
##
## $`cellular response to vitamin D`
## [1] "Sfrp1"
##
## $`regulation of fibroblast apoptotic process`
## [1] "Sfrp1"
##
## $`response to X-ray`
## [1] "Sfrp1"
##
## $`negative regulation of tissue remodeling`
## [1] "Sfrp1"
##
## $`regulation of androgen receptor signaling pathway`
## [1] "Sfrp1"
##
## $`regulation of non-canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`fibroblast apoptotic process`
## [1] "Sfrp1"
##
## $`trabecula formation`
## [1] "Sfrp1"
##
## $`cellular response to vitamin`
## [1] "Sfrp1"
##
## $`regulation of osteoblast proliferation`
## [1] "Sfrp1"
##
## $`Wnt signaling pathway, planar cell polarity pathway`
## [1] "Sfrp1"
##
## $`prostate gland epithelium morphogenesis`
## [1] "Sfrp1"
##
## $`prostate gland morphogenesis`
## [1] "Sfrp1"
##
## $`axis elongation`
## [1] "Sfrp1"
##
## $`response to vitamin D`
## [1] "Sfrp1"
##
## $`response to prostaglandin E`
## [1] "Sfrp1"
##
## $`negative regulation of B cell activation`
## [1] "Sfrp1"
##
## $`osteoblast proliferation`
## [1] "Sfrp1"
##
## $`cellular response to estradiol stimulus`
## [1] "Sfrp1"
##
## $`establishment of planar polarity`
## [1] "Sfrp1"
##
## $`establishment of tissue polarity`
## [1] "Sfrp1"
##
## $`type B pancreatic cell proliferation`
## [1] "Sfrp1"
##
## $`regulation of B cell differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of epithelial to mesenchymal transition`
## [1] "Sfrp1"
##
## $`negative regulation of JNK cascade`
## [1] "Sfrp1"
##
## $`negative regulation of osteoclast differentiation`
## [1] "Sfrp1"
##
## $`cellular response to estrogen stimulus`
## [1] "Sfrp1"
##
## $`negative regulation of intracellular steroid hormone receptor signaling pathway`
## [1] "Sfrp1"
##
## $`response to prostaglandin`
## [1] "Sfrp1"
##
## $`positive regulation of smoothened signaling pathway`
## [1] "Sfrp1"
##
## $`hematopoietic stem cell differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of fibroblast proliferation`
## [1] "Sfrp1"
##
## $`negative regulation of ossification`
## [1] "Sfrp1"
##
## $`androgen receptor signaling pathway`
## [1] "Sfrp1"
##
## $`dopaminergic neuron differentiation`
## [1] "Sfrp1"
##
## $`regulation of extrinsic apoptotic signaling pathway via death domain receptors`
## [1] "Sfrp1"
##
## $`midbrain development`
## [1] "Sfrp1"
##
## $`negative regulation of peptidyl-tyrosine phosphorylation`
## [1] "Sfrp1"
##
## $`cellular response to nutrient`
## [1] "Sfrp1"
##
## $`negative regulation of MAP kinase activity`
## [1] "Sfrp1"
##
## $`trabecula morphogenesis`
## [1] "Sfrp1"
##
## $`digestive tract morphogenesis`
## [1] "Sfrp1"
##
## $`prostate gland development`
## [1] "Sfrp1"
##
## $`negative regulation of BMP signaling pathway`
## [1] "Sfrp1"
##
## $`non-canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`morphogenesis of a polarized epithelium`
## [1] "Sfrp1"
##
## $`negative regulation of myeloid leukocyte differentiation`
## [1] "Sfrp1"
##
## $`regulation of bone remodeling`
## [1] "Sfrp1"
##
## $`regulation of JUN kinase activity`
## [1] "Sfrp1"
##
## $`negative regulation of lymphocyte differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of insulin secretion`
## [1] "Sfrp1"
##
## $`regulation of morphogenesis of a branching structure`
## [1] "Sfrp1"
##
## $`positive regulation of extrinsic apoptotic signaling pathway`
## [1] "Sfrp1"
##
## $`positive regulation of fat cell differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of osteoblast differentiation`
## [1] "Sfrp1"
##
## $`regulation of morphogenesis of an epithelium`
## [1] "Sfrp1"
##
## $`urogenital system development`
## [1] "Sfrp1"
##
## $somitogenesis
## [1] "Sfrp1"
##
## $`negative regulation of peptide hormone secretion`
## [1] "Sfrp1"
##
## $`negative regulation of peptide secretion`
## [1] "Sfrp1"
##
## $`regulation of intracellular steroid hormone receptor signaling pathway`
## [1] "Sfrp1"
##
## $`cellular response to interleukin-1`
## [1] "Sfrp1"
##
## $`cellular response to ionizing radiation`
## [1] "Sfrp1"
##
## $`extrinsic apoptotic signaling pathway via death domain receptors`
## [1] "Sfrp1"
##
## $`regulation of tissue remodeling`
## [1] "Sfrp1"
##
## $`somatic stem cell population maintenance`
## [1] "Sfrp1"
##
## $`regulation of osteoclast differentiation`
## [1] "Sfrp1"
##
## $`somite development`
## [1] "Sfrp1"
##
## $`negative regulation of protein serine/threonine kinase activity`
## [1] "Sfrp1"
##
## $`response to vitamin`
## [1] "Sfrp1"
##
## $`negative regulation of myeloid cell differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of protein secretion`
## [1] "Sfrp1"
##
## $`dorsal/ventral pattern formation`
## [1] "Sfrp1"
##
## $`regulation of smoothened signaling pathway`
## [1] "Sfrp1"
##
## $`neural crest cell differentiation`
## [1] "Sfrp1"
##
## $`substrate adhesion-dependent cell spreading`
## [1] "Sfrp1"
##
## $`regulation of animal organ morphogenesis`
## [1] "Sfrp1"
##
## $`response to interleukin-1`
## [1] "Sfrp1"
##
## $`axis specification`
## [1] "Sfrp1"
##
## $`response to estrogen`
## [1] "Sfrp1"
##
## $`negative regulation of hormone secretion`
## [1] "Sfrp1"
##
## $`neural tube closure`
## [1] "Sfrp1"
##
## $`regulation of epithelial to mesenchymal transition`
## [1] "Sfrp1"
##
## $`regulation of BMP signaling pathway`
## [1] "Sfrp1"
##
## $`tube closure`
## [1] "Sfrp1"
##
## $`negative regulation of cellular response to growth factor stimulus`
## [1] "Sfrp1"
##
## $`bone remodeling`
## [1] "Sfrp1"
##
## $`positive regulation of canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`cellular response to fibroblast growth factor stimulus`
## [1] "Sfrp1"
##
## $`ureteric bud development`
## [1] "Sfrp1"
##
## $`primary neural tube formation`
## [1] "Sfrp1"
##
## $`mesonephric epithelium development`
## [1] "Sfrp1"
##
## $`mesonephric tubule development`
## [1] "Sfrp1"
##
## $segmentation
## [1] "Sfrp1"
##
## $`response to fibroblast growth factor`
## [1] "Sfrp1"
##
## $`mesonephros development`
## [1] "Sfrp1"
##
## $`nuclear receptor-mediated steroid hormone signaling pathway`
## [1] "Sfrp1"
##
## $`response to estradiol`
## [1] "Sfrp1"
##
## $`negative regulation of leukocyte differentiation`
## [1] "Sfrp1"
##
## $`regulation of fibroblast proliferation`
## [1] "Sfrp1"
##
## $`neural tube formation`
## [1] "Sfrp1"
##
## $`steroid hormone receptor signaling pathway`
## [1] "Sfrp1"
##
## $`negative regulation of hemopoiesis`
## [1] "Sfrp1"
##
## $`female gonad development`
## [1] "Sfrp1"
##
## $`osteoclast differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`development of primary female sexual characteristics`
## [1] "Sfrp1"
##
## $`positive regulation of Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`negative regulation of protein transport`
## [1] "Sfrp1"
##
## $`regulation of ossification`
## [1] "Sfrp1"
##
## $`digestive tract development`
## [1] "Sfrp1"
##
## $`regulation of B cell activation`
## [1] "Sfrp1"
##
## $`regulation of fat cell differentiation`
## [1] "Sfrp1"
##
## $`embryonic epithelial tube formation`
## [1] "Sfrp1"
##
## $`regulation of myeloid leukocyte differentiation`
## [1] "Sfrp1"
##
## $`fibroblast proliferation`
## [1] "Sfrp1"
##
## $`negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Sfrp1"
##
## $`response to ionizing radiation`
## [1] "Sfrp1"
##
## $`B cell differentiation`
## [1] "Sfrp1"
##
## $`regulation of MAP kinase activity`
## [1] "Sfrp1"
##
## $`cellular response to hypoxia`
## [1] "Sfrp1"
##
## $`gland morphogenesis`
## [1] "Sfrp1"
##
## $`digestive system development`
## [1] "Sfrp1"
##
## $`negative regulation of establishment of protein localization`
## [1] "Sfrp1"
##
## $`regulation of osteoblast differentiation`
## [1] "Sfrp1"
##
## $`regulation of JNK cascade`
## [1] "Sfrp1"
##
## $`epithelial tube formation`
## [1] "Sfrp1"
##
## $`smoothened signaling pathway`
## [1] "Sfrp1"
##
## $`female sex differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`negative regulation of epithelial cell proliferation`
## [1] "Sfrp1"
##
## $`epithelial to mesenchymal transition`
## [1] "Sfrp1"
##
## $`BMP signaling pathway`
## [1] "Sfrp1"
##
## $`kidney epithelium development`
## [1] "Sfrp1"
##
## $`regulation of extrinsic apoptotic signaling pathway`
## [1] "Sfrp1"
##
## $`negative regulation of protein kinase activity`
## [1] "Sfrp1"
##
## $`response to nutrient`
## [1] "Sfrp1"
##
## $`negative regulation of lymphocyte activation`
## [1] "Sfrp1"
##
## $`nuclear receptor-mediated signaling pathway`
## [1] "Sfrp1"
##
## $`tube formation`
## [1] "Sfrp1"
##
## $`negative regulation of MAPK cascade`
## [1] "Sfrp1"
##
## $`positive regulation of apoptotic signaling pathway`
## [1] "Sfrp1"
##
## $`morphogenesis of embryonic epithelium`
## [1] "Sfrp1"
##
## $`response to BMP`
## [1] "Sfrp1"
##
## $`cellular response to BMP stimulus`
## [1] "Sfrp1"
##
## $`male gonad development`
## [1] "Sfrp1"
##
## $`cellular response to ketone`
## [1] "Sfrp1"
##
## $`development of primary male sexual characteristics`
## [1] "Sfrp1"
##
## $`cellular response to alcohol`
## [1] "Sfrp1"
##
## $`cellular response to radiation`
## [1] "Sfrp1"
##
## $`hematopoietic progenitor cell differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of kinase activity`
## [1] "Sfrp1"
##
## $`cellular response to decreased oxygen levels`
## [1] "Sfrp1"
##
## $`neural tube development`
## [1] "Sfrp1"
##
## $`negative regulation of cell growth`
## [1] "Sfrp1"
##
## $`JNK cascade`
## [1] "Sfrp1"
##
## $`negative regulation of secretion by cell`
## [1] "Sfrp1"
##
## $`negative regulation of leukocyte activation`
## [1] "Sfrp1"
##
## $`cellular response to starvation`
## [1] "Sfrp1"
##
## $`cellular response to tumor necrosis factor`
## [1] "Sfrp1"
##
## $gastrulation
## [1] "Sfrp1"
##
## $`hormone-mediated signaling pathway`
## [1] "Sfrp1"
##
## $`cellular response to oxygen levels`
## [1] "Sfrp1"
##
## $`positive regulation of cell growth`
## [1] "Sfrp1"
##
## $`negative regulation of transferase activity`
## [1] "Sfrp1"
##
## $`male sex differentiation`
## [1] "Sfrp1"
##
## $`cellular response to steroid hormone stimulus`
## [1] "Sfrp1"
##
## $`negative regulation of secretion`
## [1] "Sfrp1"
##
## $`tissue remodeling`
## [1] "Sfrp1"
##
## $`stem cell population maintenance`
## [1] "Sfrp1"
##
## $`negative regulation of cell activation`
## [1] "Sfrp1"
##
## $`regulation of reproductive process`
## [1] "Sfrp1"
##
## $`response to tumor necrosis factor`
## [1] "Sfrp1"
##
## $`regulation of insulin secretion`
## [1] "Sfrp1"
##
## $`morphogenesis of a branching epithelium`
## [1] "Sfrp1"
##
## $`maintenance of cell number`
## [1] "Sfrp1"
##
## $`regulation of lymphocyte differentiation`
## [1] "Sfrp1"
##
## $`regulation of myeloid cell differentiation`
## [1] "Sfrp1"
##
## $`anterior/posterior pattern specification`
## [1] "Sfrp1"
##
## $`positive regulation of epithelial cell proliferation`
## [1] "Sfrp1"
##
## $`osteoblast differentiation`
## [1] "Sfrp1"
##
## $`response to starvation`
## [1] "Sfrp1"
##
## $`regulation of peptidyl-tyrosine phosphorylation`
## [1] "Sfrp1"
##
## $`regulation of neuron differentiation`
## [1] "Sfrp1"
##
## $`extrinsic apoptotic signaling pathway`
## [1] "Sfrp1"
##
## $`morphogenesis of a branching structure`
## [1] "Sfrp1"
##
## $`central nervous system neuron differentiation`
## [1] "Sfrp1"
##
## $`negative regulation of growth`
## [1] "Sfrp1"
##
## $`negative regulation of protein localization`
## [1] "Sfrp1"
##
## $`regulation of canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`mesenchymal cell differentiation`
## [1] "Sfrp1"
##
## $`regulation of protein serine/threonine kinase activity`
## [1] "Sfrp1"
##
## $`skeletal system morphogenesis`
## [1] "Sfrp1"
##
## $`fat cell differentiation`
## [1] "Sfrp1"
##
## $`insulin secretion`
## [1] "Sfrp1"
##
## $`cellular response to nutrient levels`
## [1] "Sfrp1"
##
## $`regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Sfrp1"
##
## $`regulation of peptide hormone secretion`
## [1] "Sfrp1"
##
## $`regulation of peptide secretion`
## [1] "Sfrp1"
##
## $`cellular response to transforming growth factor beta stimulus`
## [1] "Sfrp1"
##
## $`regulation of peptide transport`
## [1] "Sfrp1"
##
## $`developmental growth involved in morphogenesis`
## [1] "Sfrp1"
##
## $`response to transforming growth factor beta`
## [1] "Sfrp1"
##
## $`myeloid leukocyte differentiation`
## [1] "Sfrp1"
##
## $`gonad development`
## [1] "Sfrp1"
##
## $`stem cell differentiation`
## [1] "Sfrp1"
##
## $`peptidyl-tyrosine phosphorylation`
## [1] "Sfrp1"
##
## $`development of primary sexual characteristics`
## [1] "Sfrp1"
##
## $`peptidyl-tyrosine modification`
## [1] "Sfrp1"
##
## $`canonical Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`negative regulation of cell development`
## [1] "Sfrp1"
##
## $`cell fate commitment`
## [1] "Sfrp1"
##
## $`negative regulation of protein phosphorylation`
## [1] "Sfrp1"
##
## $`response to ketone`
## [1] "Sfrp1"
##
## $`B cell activation`
## [1] "Sfrp1"
##
## $`positive regulation of growth`
## [1] "Sfrp1"
##
## $`negative regulation of cell migration`
## [1] "Sfrp1"
##
## $`mesenchyme development`
## [1] "Sfrp1"
##
## $`regulation of Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`peptide hormone secretion`
## [1] "Sfrp1"
##
## $`regulation of cellular response to growth factor stimulus`
## [1] "Sfrp1"
##
## $`negative regulation of phosphorylation`
## [1] "Sfrp1"
##
## $`peptide secretion`
## [1] "Sfrp1"
##
## $`regulation of protein secretion`
## [1] "Sfrp1"
##
## $`negative regulation of cell motility`
## [1] "Sfrp1"
##
## $`response to hypoxia`
## [1] "Sfrp1"
##
## $`regulation of hormone secretion`
## [1] "Sfrp1"
##
## $`peptide transport`
## [1] "Sfrp1"
##
## $`response to steroid hormone`
## [1] "Sfrp1"
##
## $`negative regulation of locomotion`
## [1] "Sfrp1"
##
## $`transforming growth factor beta receptor superfamily signaling pathway`
## [1] "Sfrp1"
##
## $`sex differentiation`
## [1] "Sfrp1"
##
## $`regulation of leukocyte differentiation`
## [1] "Sfrp1"
##
## $`kidney development`
## [1] "Sfrp1"
##
## $`cell-substrate adhesion`
## [1] "Sfrp1"
##
## $`response to decreased oxygen levels`
## [1] "Sfrp1"
##
## $`response to alcohol`
## [1] "Sfrp1"
##
## $`reproductive structure development`
## [1] "Sfrp1"
##
## $`negative regulation of phosphorus metabolic process`
## [1] "Sfrp1"
##
## $`intracellular receptor signaling pathway`
## [1] "Sfrp1"
##
## $`negative regulation of phosphate metabolic process`
## [1] "Sfrp1"
##
## $`renal system development`
## [1] "Sfrp1"
##
## $`reproductive system development`
## [1] "Sfrp1"
##
## $`cellular response to abiotic stimulus`
## [1] "Sfrp1"
##
## $`cellular response to environmental stimulus`
## [1] "Sfrp1"
##
## $`epithelial tube morphogenesis`
## [1] "Sfrp1"
##
## $`cell surface receptor protein serine/threonine kinase signaling pathway`
## [1] "Sfrp1"
##
## $`amide transport`
## [1] "Sfrp1"
##
## $`hormone secretion`
## [1] "Sfrp1"
##
## $`negative regulation of protein modification process`
## [1] "Sfrp1"
##
## $`hormone transport`
## [1] "Sfrp1"
##
## $`regulation of epithelial cell proliferation`
## [1] "Sfrp1"
##
## $`protein secretion`
## [1] "Sfrp1"
##
## $`response to oxygen levels`
## [1] "Sfrp1"
##
## $`establishment of protein localization to extracellular region`
## [1] "Sfrp1"
##
## $`regulation of apoptotic signaling pathway`
## [1] "Sfrp1"
##
## $`protein localization to extracellular region`
## [1] "Sfrp1"
##
## $regionalization
## [1] "Sfrp1"
##
## $`regulation of cell growth`
## [1] "Sfrp1"
##
## $`regulation of hemopoiesis`
## [1] "Sfrp1"
##
## $`Wnt signaling pathway`
## [1] "Sfrp1"
##
## $`lymphocyte differentiation`
## [1] "Sfrp1"
##
## $`response to radiation`
## [1] "Sfrp1"
##
## $`regulation of protein kinase activity`
## [1] "Sfrp1"
##
## $`response to xenobiotic stimulus`
## [1] "Sfrp1"7.3 Type 4 Downregulated lowsalt
# Arrange and filter DEGs for type 4
df <- type_4 %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers4down <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columnsmarkers4down <- ENTREZ_list %>% inner_join(markers4down, by = "SYMBOL")
markers4down <- markers4down %>% dplyr::filter(p_val_adj < 0.05)
#head(markers4down, n = 50)
pos.markers4down <- markers4down %>% dplyr::filter(avg_log2FC < 0) %>% arrange(desc(abs(avg_log2FC)))
# Adjust avg_log2FC threshold here if you want a stricter cutoff
pos.ranks4down <- pos.markers4down$ENTREZID[abs(pos.markers4down$avg_log2FC) > 0]
#head(pos.ranks4down)
pos_go4down <- enrichGO(
gene = pos.ranks4down, # a vector of entrez gene id
OrgDb = org.Mm.eg.db,
ont = "BP",
readable = TRUE # whether mapping gene ID to gene Name
)
pos_go4down## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:2] "17750" "17748"
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...18 enriched terms found
## 'data.frame': 18 obs. of 12 variables:
## $ ID : chr "GO:0097501" "GO:0061687" "GO:0071280" "GO:0071294" ...
## $ Description : chr "stress response to metal ion" "detoxification of inorganic compound" "cellular response to copper ion" "cellular response to zinc ion" ...
## $ GeneRatio : chr "2/2" "2/2" "2/2" "2/2" ...
## $ BgRatio : chr "13/28928" "16/28928" "18/28928" "20/28928" ...
## $ RichFactor : num 0.154 0.125 0.111 0.1 0.069 ...
## $ FoldEnrichment: num 2225 1808 1607 1446 998 ...
## $ zScore : num 66.7 60.1 56.7 53.8 44.6 ...
## $ pvalue : num 1.86e-07 2.87e-07 3.66e-07 4.54e-07 9.70e-07 ...
## $ p.adjust : num 2.04e-06 2.04e-06 2.04e-06 2.04e-06 2.84e-06 ...
## $ qvalue : logi NA NA NA NA NA NA ...
## $ geneID : chr "Mt2/Mt1" "Mt2/Mt1" "Mt2/Mt1" "Mt2/Mt1" ...
## $ Count : int 2 2 2 2 2 2 2 2 2 2 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722chart4down <- dotplot(pos_go4down) +
ggtitle("type 4 downregulated lowsalt") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)
) +
scale_y_discrete(
position = "right",
labels = function(x) str_wrap(x, width = 25)
) # Wrap y-axis labels to 2 lines## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.